Infections of Cathay pilots show ‘highly similar’ genetic sequencing

Two Cathay Pacific pilots whose Covid-19 infections sparked concerns over Hong Kong’s quarantine exemption policies have been confirmed to have the more transmissive Delta variant, with “highly similar but not identical” genetic sequencing.

The Centre for Health Protection yesterday also revealed a traveller who sat near the city’s first patient with the virus’ “Delta Plus” variant on a flight also carried that strain, raising concerns over whether in-flight transmission had taken place.

The two pilots, who were among Wednesday’s confirmed cases, had infections that belonged to a sub-lineage of the Delta variant called “AY.43”, authorities said.

“Both of them were Delta strain with highly similar but not identical genetic sequences,” the centre said, adding the variant was commonly seen in Europe, and the two might have been infected outside the city.

Professor Leo Poon Lit-man, who was involved in the genome sequencing analysis, said the findings suggested the pair could have caught the virus from the same source.

“If there are slight differences between them, we cannot rule out that they acquired the virus from the same source at the same time,” said Poon, head of the University of Hong Kong’s public health laboratory sciences division. He added if the virus had been passed from one pilot to another, the genetic sequencing should have been identical.

Genome sequencing by the centre also revealed a 56-year-old man who arrived from Britain on November 1 and became a confirmed case on Sunday was the second patient in the city to carry the “Delta Plus” variant.

He was sitting in seat 2B on flight BA027, near the first Delta Plus patient, a 62-year-old man.

While epidemiological investigation was continuing, Poon said previous cases showed in-flight transmission occurred before.

Government pandemic adviser Professor David Hui Shucheong said not much data was available on the two Delta strain sub-lineages but there was “no need to be worried right now” because they had not been classified as a variant of concern.

Hui also said the Transport and Housing Bureau should reexamine its quarantine exemption policy. “If there are no changes, next time we may not be as lucky. Aircrew may need to undergo a short quarantine, maybe a week, to be safer,” he said.

“If there are no local infections over the next 14 days, then Hong Kong can count itself lucky.”

The latest developments came as the city confirmed three more imported Covid-19 cases, travellers from the Philippines, Thailand and Saudi Arabia.

The additions took the official tally of confirmed cases to 12,377, with 213 related deaths.

Thirty-seven recovered patients, meanwhile, were sent to the Dorsett Kwun Tong hotel, which has replaced the North Lantau Hospital Hong Kong Infection Control Centre as the designated venue for the 14-day, post-recovery quarantine now mandated by government policy.

With the start of the city’s booster programme yesterday, queues formed outside coronavirus vaccination centres, with eligible residents – currently the elderly and other high-risk groups – eager to boost their immunity against Covid-19 with a third jab.

An advisory panel on vaccines is expected to discuss next Monday whether to lower the minimum vaccination age of the Chinese-made Sinovac vaccine, according to member Professor Lau Yu-lung. Sinovac last month submitted an application to the government to lower the minimum age from 18 to three.

Some 16,825 people received booster shots, including Chief Executive Carrie Lam Cheng Yuet-ngor, health minister Sophia Chan Siu-chee and civil service chief Patrick Nip Tak-kuen.